摘要:

Studies of binding of substrates and inhibitors of the enzymed‐xylose isomerase show, from X‐ray diffraction data at 1.6–1.9 Å resolution, that there are a variety of binding modes. These vary in the manner in which the substrate or its analogue extend, on binding, across the carboxy end of the (βα)8‐barrel structure. These binding sites are His54 and the metal ion (magnesium or manganese) that is held in place by Glul81, Asp245, Glu217 and Asp287. Possible catalytic groups have been identified in proposed mechanisms and their role in the binding of ligands is

ISSN:1399-0047    

DOI:10.1107/S0907444993009345

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Glucose isomerase fromStreptomyces murinushas been crystallized in space groupP41212, cell dimensionsa=b= 137.65 andc= 132.20 Å. One dimer of the tetrametric molecule is found per asymmetric unit. An initial structure solution was obtained by the molecular replacement method. The crystallographic refinement was performed using molecular dynamics techniques with X‐ray restraints. The final crystallographicRvalue is 21.4% at 2.6 Å resolution including 3023 non‐H atoms, two metal ions and two water molecules pe

ISSN:1399-0047    

DOI:10.1107/S0907444993009540

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

A recently reported method – the improved condensing protocol [Subbiah (1991).Science,252, 128–133; (1993).Acta Cryst. D49, 108119] – for obtaining low‐resolution macromolecular envelopes is applied to five varied test cases. These examples were chosen to illustrate the general applicability of the method to the wide range that typical macromolecular crystals adopt. The cases include small and large asymmetric unit volumes (4.7 × 104to 1.17 × 106 Å3), low and high symmetry (2 to 12 symmetry elements), small and large proteins (1570 to 12 216 non‐H atoms), orthogonal and non‐orthogonal unit cells, a wide variety of space groups (P21toP6322), small and large solvent contents (33–80%), and a case of non‐crystallographic symmetry (threefold). In all five cases the inherent ambiguity of the condensing protocol in differentiating between bulk matter and bulk solvent is then resolved by use of the recently reported sign‐fixin

ISSN:1399-0047    

DOI:10.1107/S090744499301131X

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Trypanothione reductase is an FAD‐dependent disulfide oxidoreductase which catalyses the reduction of trypanothione using NADPH as co‐factor. The enzyme is unique to protozoan parasites from the generaTrypanosomaandLeishmaniaand is an important target for the design of improved antitrypanocidal drugs. We present details of the structure of trypanothione reductase fromCrithidia fasciculatasolved by molecular replacement, using human glutathione reductase as a search model, and refined to anRfactor of 16.1% with data between 8.0 and 2.6 Å resolution. The model comprises two subunits (one containing 487 residues, the other 486), an FAD prosthetic group, plus 392 solvent molecules. The last four C‐terminal residues are not seen in either subunit and the density is poor for the N‐terminal residue of subunitB. The model has a root‐mean‐square deviation from ideality of 0.016 Å for bond lengths and 3.2° for bond angles. Each subunit was independently refined in the latter stages of the analysis but the subunits remain similar as indicated by the root‐mean‐square deviation of 0.35 Å for Cαatoms. Trypanothione reductase has 36% sequence identity with human glutathione reductase and the root‐mean‐square deviation between the 462 Cαatoms in the secondary structural units common to the two proteins is 1.1 Å. However, there are large differences in the loop regions and significant shifts in the orientation of the four domains within each subunit. Domain II, which binds the dinucleotide co‐factor, and domain IV, which forms the interface between the two subunits, are both rotated by approximately 5° with respect to domain I, which binds the FAD moiety, when compared with glutathione reductase. Crystals of trypanothione reductase have been soaked in the dinucleotide co‐factor NADPH andN1‐glutathionylspermidine disulfide substrate and the structure of the resulting complex determined at 2.8 Å resolution. Strong density is observed for the adenosine end of the co‐factor which forms many charged interactions with the protein though the density for the nicotinamide moiety is more diffuse. The mode of binding indicates that NADP is bound to the enzyme in a similar conformation to

ISSN:1399-0047    

DOI:10.1107/S0907444993011898

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Methods to assist in the spatial and visual analysis of electron‐density maps have been investigated as part of a project in molecular scene analysis [Fortier, Castleden, Glasgow, Conklin, Walmsley, Leherte&Allen (1993).Acta Cryst. D49, 168178]. In particular, the usefulness of the topological approach for the segmentation of medium‐resolution (3 Å) maps of proteins and their interpretation in terms of structural motifs has been assessed. The approach followed is that proposed by Johnson [Johnson (1977).ORCRIT.The Oak Ridge Critical Point Network Program. Chemistry Division, Oak Ridge National Laboratory, USA] which provides a global representation of the electron‐density distribution through the location, identification and linkage of its critical points. In the first part of the study, the topological approach was applied to calculated maps of three proteins of small to medium size so as to develop a methodology that could then be used for analyzing maps of medium resolution. The methodology was then applied to both calculated and experimental maps of penicillopepsin at 3 Å resolution. The study shows that the networks of critical points can provide a useful segmentation of the maps, tracing the protein main chains and capturing their conformation. In addition, these networks can be parsed in terms of secondary‐structure motifs, through a geometrical analysis of the critical points. The procedure adopted for secondary‐structure recognition, which was phrased in terms of geometry‐based rules, provides a basis for a further automated implementation of a more complete set of recognition operations through the use of artificial‐inte

ISSN:1399-0047    

DOI:10.1107/S0907444993011345

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Ferredoxin I (Fd I) fromEquisetum arvenseis an iron–sulfur protein composed of 95 amino‐acid residues and one [2Fe–2S] cluster. It crystallized in the space groupP21,a= 30.4,b= 57.4,c= 47.5 Å and β = 78.7° with two molecules per asymmetric unit. X‐ray diffraction data up to 1.8 Å resolution were collected by using a Rigaku four‐circle diffractometer. The initial model of Fd I, which was derived by the molecular replacement method using a structure of the Fd I from the blue–green algaAphanothece sacrum, was refined by molecular dynamics simulation and a least‐squares minimization with stereochemical restraints. Positional parameters and isotropic temperature factors for 1420 non‐H protein atoms and 183 water molecules were refined on 13 838 observed structure factors (Fo>σFo) between 10.0 and 1.8 Å resolution. The finalRfactor was 17.0%, and the standard deviation of atomic position estimated by Luzzati plot [Luzzati (1952).Acta Cryst.5, 802810] was 0.2 Å. The electron‐density map was well defined for the two independent molecules except for the N‐terminal residue and the three C‐terminal residues. Equivalent Cα atoms of two independent molecules in the asymmetric unit were superposed by the least‐squares method with root‐mean‐square deviations of 0.26 Å. Reasonable structural differences were observed at a polypeptide segment having few intramolecular interactions. Highly flexible regions of the molecule were assigned from the structural differences between the two independent molecules in the crystal and the distribution of

ISSN:1399-0047    

DOI:10.1107/S0907444993009588

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Putrescine is the immediate precursor for the synthesis of polyamines and is normally generated by the action of ornithine decarboxylase. However, putrescine can also be produced by the conversion of arginine to agmatine by arginine decarboxylase (bADC) followed by the release of urea by agmatine ureohydrolase. Amino‐acid sequence homology with the eukaryotic ornithine decarboxylases suggests that bADC may be a model for this group of decarboxylases. We report here the crystallization of arginine decarboxylase fromE. coli. Crystals up to 1 mm in size are grown by vapor equilibration using Li2SO4and polyethylene glycols as precipitants. The crystals exhibit diffraction maxima beyond 3 Å resolution and belong to space groupP41(3)212 witha= 192.4 andc= 121.0 Å. These unit‐cell dimensions together with the estimated density of the crystals suggest the presence of one tetramer of bADC (71 kDa subunit−1) per asymmetric unit

ISSN:1399-0047    

DOI:10.1107/S0907444993009989

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

A computer program,VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling programO. Additionally,VOIDOOcan be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed usingO. Examples of the use ofVOIDOOare given forP2 myelin protein, cellular retinol‐binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are give

ISSN:1399-0047    

DOI:10.1107/S0907444993011333

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The metal cluster Ta6Br14has been used to prepare heavy‐metal derivatives of two large proteins, ribulose‐1,5‐bisphosphate carboxylase/oxygenase and transketolase. In both cases, this cluster compound produced a single‐site derivative for which a difference Patterson map, calculated to 5.5 Å resolution, could be solved straightforwardly. Ta6Br14provided enough phase information to unambiguously locate the heavy‐atom positions in other multiple‐site derivatives. In transketolase, the heavy‐metal complex binds at the surface of the protein in a dominantly hydrophobic pocket. In ribulose bisphosphate carboxylase/oxygenase, it binds between two molecules in the crystal lattice. There are negatively charged glutamic and/or aspartic acid residues in the vicinity of the bound clusters. Ta6Br14is useful over a wide range of pH. For large proteins and/or large unit cells, this compound should be included in the initial screening for heavy

ISSN:1399-0047    

DOI:10.1107/S0907444993009679

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The X‐ray diffraction pattern of the crystals of the non‐selfcomplementary hexadeoxyribonucleotide d(CGCACG)·d(CGTGCG) can be indexed in four different space groups: (i)P65andP21, with cell parametersa= 17.75 (1),b= 17.76 (1),c= 42.77 (3) Å, α = 90, β = 90, γ = 120°, and (ii)P212121andC2, with cell parametersa= 17.75 (1),b= 30.74 (2),c= 42.77 (3) Å, α = 90, β = 90, γ = 90°. While theRmergefor the equivalent reflections in the different space groups indicates thatP21is the correct choice in the present case, it is demonstrated that the near degeneracy of the space groups arises out of the fact that the DNA molecule is nearly cylindrical. A perfect cylinder

ISSN:1399-0047    

DOI:10.1107/S0907444993011035

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY